AMBER Archive (2004)

Subject: RE: AMBER: long minimization in sander

From: Ross Walker (
Date: Mon Oct 25 2004 - 10:11:29 CDT

Hi Murat
> Can long minimizations cause unreasonable operation in MD
> simulations with sander?

No, they should not give any problems. You just waste time doing 'too' much

> The problem is: I have made 2000O steps of min prior to my
> 1ns MD at 600K and it
> worked good. However, I wanted to use my same minimized
> system prior to my 300K
> MD but it just terminates at the beginning. This happens both
> in vacuum and
> explicit solvent environment...

What do you mean by "just terminates at the beginning?" What is the error
message. Without more info we cannot help you here. It is most likely an
error in your mdin file that is causing the problem rather than with the
restrt file from minimisation. Please post your mdin and any error messages
written to the screen or mdout.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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